The labeling of nucleic acids with detectable probes has been a common molecular biology laboratory technique for decades. In recent years, the development and commercial success of nucleic acid microarrays (sometimes also called biochips) has often relied, in part, on the use of labeled nucleic acid probes.
Many nucleic acid labeling techniques require indirect labeling; in other words, the nucleic acids are labeled with one member of a specific binding pair (e.g., biotin), hybridized to a target nucleic acid, and visualized with the other member of the specific binding pair which is detectably labeled (e.g., horseradish peroxidase-labeled streptavidin). Direct labeling of nucleic acids has recently been achieved using bisulfite-catalyzed transamination (BCT) of cytidines within a nucleic acid (U.S. Pat. Nos. 5,506,350 and 5,491,224). However, these direct labeling procedures, performed in solution, are limited by the time (two or more days) required to achieve sufficient labeling of the nucleic acids.
Oligonucleotides are commonly made today using a solid phase methodology in which the oligos are prepared by successive iterative additions of nucleoside monomers while the growing oligonucleotide chain is attached to a solid phase. Oligonucleotides have been modified with single or multiple fluorescent dye molecules while still attached to the synthesis solid phase, e.g., as described in Haralambidis et al., Nuc. Acids Res., 18:501-505, 1990. However, this methodology cannot be applied to complex genomic DNAs such as that extracted from solid tumor samples or blood samples.